B. I think it is calculated separately for each casting class. It's not really an ongoing effect, since it can't be dispelled, etc. So you can't really invoke the stacking rules.
Since it's not an ongoing effect, it shouldn't have memory of which class/CL/etc. casts the spell.
Let's say you're Wiz 1/Clr 3/MT 6, so your Wizard level is 7, Cleric level is 9. No Practiced Spellcaster.
Cast Animate Dead from your Wizard 7 side to animate 10 HD of undead, you now have 10/28 HD of undead under your control.
Cast Animate Dead from your Cleric 9 side to animate 15 more HD of undead, you now have 25/36 HD of undead under your control via Animate Dead. There's no check to see if it was your Wizard side or Cleric side casting the spell the first time.
Cast Animate Dead from your Wizard 7 side again to animate 10 more HD of undead. This is where it gets weird, as you now either have 35/36 HD commanded or 35/28 HD commanded, and have to choose and let go of 7 HD of undead previously commanded. By my interpretation, I think the latter actually happens.